IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    holy7c18501.rc.fas.harvard.edu (AVX512, FMA3, 188 GB RAM)
Command: iqtree2 -s /n/holylfs04/LABS/giribet_lab/Lab/tammy/pera_all_21k/taxon-sets/vD/concat_75/concat_75_wo_pta.nexus -m MFP+MERGE -p /n/holylfs04/LABS/giribet_lab/Lab/tammy/pera_all_21k/taxon-sets/vD/concat_75/partitions_iqtree.txt -rcluster 10 -bb 1500 -alrt 1500 -nt AUTO -pre astral_pta_75p
Seed:    194023 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Sep 18 06:53:29 2025
Kernel:  AVX+FMA - auto-detect threads (11 CPU cores detected)

Reading partition model file /n/holylfs04/LABS/giribet_lab/Lab/tammy/pera_all_21k/taxon-sets/vD/concat_75/partitions_iqtree.txt ...
Reading alignment file /n/holylfs04/LABS/giribet_lab/Lab/tammy/pera_all_21k/taxon-sets/vD/concat_75/concat_75_wo_pta.nexus ... Nexus format detected
Alignment has 70 sequences with 1996 columns, 1332 distinct patterns
901 parsimony-informative, 285 singleton sites, 810 constant sites
                                           Gap/Ambiguity  Composition  p-value
   1  Acanthaspidiidae_Actp_MCZ172845              0.75%    passed     96.34%
   2  Acanthonotozomoides_oatesi_Aoat_MCZ172843    2.10%    passed     99.59%
   3  Antarctomysis_maxima_Amax_MCZ140283         34.62%    passed     21.70%
   4  Caprella_penantis_Cpen_USNM1463333          14.73%    passed     19.78%
   5  Cyamus_boopis_CybBW1                         1.00%    passed     39.92%
   6  Cyphocaris_richardi_Crich_MCZ172829          1.40%    passed     75.22%
   7  Desmosomatidae_Desmo1_MCZ172908             17.03%    passed     96.77%
   8  Deutella_incerta_Dinc_USNM1605057            5.71%    passed     44.68%
   9  Epimeria_sp_Epim1_MCZ172924                 66.88%    passed     23.81%
  10  Eurycope_sp1_Eury1_MCZ172910                11.42%    passed     78.60%
  11  Eusiridae_Eusi1_MCZ172955                   11.82%    passed     61.88%
  12  Gnathiidae_Gnath_MCZ172918                  33.77%    passed     19.52%
  13  Haploniscus_sp_Haplo_MCZ172849               0.75%    passed     65.06%
  14  Hyachelia_tortugae_Htor1                     7.11%    passed     84.98%
  15  Iantopsis_sp_Janto_MCZ172931                68.29%    failed      0.83%
  16  Idotea_sp_Idot_MCZ166902                     0.00%    passed     50.17%
  17  Ischnomesidae_sp1_Ischno1_MCZ172929          6.46%    passed     57.80%
  18  Ischnomesidae_sp2_Ischno2_MCZ172930         15.58%    passed     82.51%
  19  Lampropidae_Lamp1_MCZ172887                 10.82%    passed     57.50%
  20  Laticorophium_baconi_Lbac_USNM1605092       34.62%    passed      5.94%
  21  Mictocaris_halope_Mhal_MCZ135174            38.43%    passed     95.02%
  22  Munnidae_sp1_Munni1_MCZ172905               32.57%    passed     43.99%
  23  Munnopsidae_sp2_Munno2_MCZ172914            12.17%    passed     88.63%
  24  Nannastacidae_Nanna1_MCZ172885              17.99%    passed     15.31%
  25  Natatolana_sp_Nata_MCZ172842                 0.55%    passed     88.53%
  26  Neoxenodice_sp_Neox_MCZ172934                0.65%    passed     89.46%
  27  Parandania_boecki_Pboe_MCZ172673            20.54%    passed     53.43%
  28  Phronima_sp_Phro                            48.75%    passed     28.78%
  29  Podocerus_brasiliensis_PbraSI_USNM1605825    0.70%    passed     57.16%
  30  Rocinela_sp_Roci                            14.33%    passed     67.67%
  31  Serolidae_Sero2_MCZ172956                    0.65%    passed     36.57%
  32  Serolidae_sp1_Sero1_MCZ172911               27.91%    passed     51.19%
  33  Tanaidacea_TanANT_MCZ172928                 20.64%    passed     69.37%
  34  Themisto_gaudichaudii_Tgau_MCZ172670        11.72%    passed     81.54%
  35  Vanhoeffenura_sp_Vanh_MCZ172827             16.73%    passed     76.16%
  36  Vibilia_sp_Vibi_MCZ172966                    3.41%    failed      1.53%
  37  Zeuxo_sp_Zeux1                               7.11%    passed     81.99%
  38  agre                                        84.57%    failed      0.33%
  39  anas                                         0.00%    passed     12.65%
  40  cmut                                        15.53%    passed     36.36%
  41  csap                                         4.96%    failed      0.27%
  42  cste                                        50.95%    passed     18.93%
  43  groe                                         0.25%    passed     49.78%
  44  hazt                                         0.35%    passed     96.99%
  45  hdan                                        22.14%    passed     10.13%
  46  hyal                                         0.35%    passed     68.90%
  47  lexo                                        52.66%    passed     27.78%
  48  maos                                         6.01%    passed     79.89%
  49  ogri                                         0.30%    passed     75.11%
  50  phaw                                         0.30%    passed     83.43%
  51  plat                                         0.30%    passed     86.03%
  52  psca                                         1.90%    passed     12.36%
  53  tlon                                         0.30%    passed     85.62%
  54  trat                                        10.62%    failed      1.19%
  55  Diastylidae_sp1_Dias1_MCZ172889             48.05%    passed     68.25%
  56  Dyopedos_sp_Dyop_USNM1644295                 7.06%    passed     49.06%
  57  Erythropinae_Eryt_MCZ172927                 36.72%    passed     36.82%
  58  Glyptonotus_antarcticus_Gant_MCZ140281      15.88%    passed     73.24%
  59  Mesosignidae_Meso1_MCZ172923                25.70%    passed     74.16%
  60  Nebalia_longicornis_Nlon_MCZ172977          27.66%    failed      0.20%
  61  Thermosbaenacea_Thermo_MCZ134138            45.34%    passed     78.89%
  62  esin                                        10.77%    failed      0.01%
  63  psed                                        17.84%    passed     17.66%
  64  tpus                                        50.75%    passed     28.26%
  65  Ampeliscidae_Ampe1_MCZ172983                63.13%    passed     36.09%
  66  Leuconidae_LeucCu_MCZ172891                 35.77%    passed     12.34%
  67  bjam                                        57.77%    passed     15.23%
  68  e_vittatus                                  82.67%    failed      1.25%
  69  Hyperia_curvicephala_Hypcur_MCZ172965       62.78%    passed     11.10%
  70  Eurythenes_obesus_Eobes_MCZ172669           94.99%    passed     44.47%
WARNING: 11 sequences contain more than 50% gaps/ambiguity
****  TOTAL                                       22.20%  8 sequences failed composition chi2 test (p-value<5%; df=3)

Partition file is not in NEXUS format, assuming RAxML-style partition file...
Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1	DNA	54	116	42	33	GTR+MERGE	uce-1041
2	DNA	54	217	116	68	GTR+MERGE	uce-1288
3	DNA	56	114	52	49	GTR+MERGE	uce-1608
4	DNA	61	94	42	20	GTR+MERGE	uce-1658
5	DNA	60	98	45	41	GTR+MERGE	uce-187
6	DNA	57	213	116	71	GTR+MERGE	uce-252
7	DNA	60	143	62	54	GTR+MERGE	uce-552
8	DNA	54	100	36	35	GTR+MERGE	uce-6
9	DNA	54	279	117	152	GTR+MERGE	uce-708
10	DNA	57	228	82	136	GTR+MERGE	uce-72
11	DNA	54	98	33	49	GTR+MERGE	uce-861
12	DNA	55	296	158	102	GTR+MERGE	uce-907
Degree of missing data: 0.200
Info: multi-threading strategy over partitions



Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.015 seconds
Measuring multi-threading efficiency up to 11 CPU cores
Increase to 10 rounds for branch lengths
37 trees examined
Threads: 1 / Time: 11.159 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -47527
Threads: 2 / Time: 7.273 sec / Speedup: 1.534 / Efficiency: 77% / LogL: -47527
Threads: 3 / Time: 5.492 sec / Speedup: 2.032 / Efficiency: 68% / LogL: -47527
Threads: 4 / Time: 4.676 sec / Speedup: 2.386 / Efficiency: 60% / LogL: -47527
Threads: 5 / Time: 4.265 sec / Speedup: 2.616 / Efficiency: 52% / LogL: -47527
Threads: 6 / Time: 5.748 sec / Speedup: 1.941 / Efficiency: 32% / LogL: -47527
BEST NUMBER OF THREADS: 5

Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Initial log-likelihood: -35411.599
Current log-likelihood at step 1: -33655.639
Current log-likelihood at step 2: -33529.209
Current log-likelihood at step 3: -33503.294
Current log-likelihood at step 4: -33490.039
Current log-likelihood at step 5: -33478.928
Current log-likelihood at step 6: -33468.080
Current log-likelihood at step 7: -33457.708
Current log-likelihood at step 8: -33315.596
Current log-likelihood at step 9: -33311.444
Parameters optimization took 8 rounds (0.561 sec)

Perform nearest neighbor interchange...
Estimate model parameters (epsilon = 1.000)
Initial log-likelihood: -33267.274
Current log-likelihood at step 1: -33264.040
Current log-likelihood at step 2: -33263.424
Partition-specific rates:  0.377 0.443 1.172 0.488 0.409 0.934 0.354 1.018 2.155 1.616 0.210 0.996
Parameters optimization took 1 rounds (0.099 sec)

Time for fast ML tree search: 0.909 seconds

NOTE: ModelFinder requires 20 MB RAM!
Selecting individual models for 12 charsets using BIC...
 No. Model        Score       TreeLen     Charset
   1 GTR+F+I+G4   10736.456   18.524      uce-708
   2 GTR+F+I+G4   6308.213    3.869       uce-1288
   3 GTR+F+I+G4   8866.256    8.921       uce-252
   4 GTR+F+I+G4   10529.676   8.824       uce-907
   5 GTR+F+I+G4   3177.662    4.697       uce-1658
   6 GTR+F+I+G4   2700.399    2.988       uce-1041
   7 GTR+F+I+G4   4120.514    3.205       uce-552
   8 GTR+F+I+G4   3740.403    10.361      uce-1608
   9 GTR+F+I+G4   2929.570    3.778       uce-187
  10 GTR+F+I+G4   3532.994    9.786       uce-6	0h:0m:0s (0h:0m:0s left)
  11 GTR+F+I+G4   1957.889    1.963       uce-861	0h:0m:0s (0h:0m:0s left)
  12 GTR+F+I+G4   8585.347    16.930      uce-72	0h:0m:0s (0h:0m:0s left)
Full partition model BIC score: 68558.990 (LnL: -33261.242  df:268)
Merging models to increase model fit (about 29 total partition schemes)...
  13 GTR+F+I+G4   68509.730   4.519       uce-1288+uce-187	0h:0m:0s (0h:0m:0s left)
  14 GTR+F+I+G4   68549.797   4.000       uce-1288+uce-552	0h:0m:0s (0h:0m:0s left)
  15 GTR+F+I+G4   68504.146   10.736      uce-6+uce-907	0h:0m:0s (0h:0m:0s left)
  16 GTR+F+I+G4   68515.866   9.835       uce-252+uce-907	0h:0m:0s (0h:0m:0s left)
  17 GTR+F+I+G4   68520.836   10.098      uce-252+uce-6	0h:0m:0s (0h:0m:0s left)
  18 GTR+F+I+G4   68556.738   3.730       uce-1041+uce-552	0h:0m:0s (0h:0m:0s left)
  19 GTR+F+I+G4   68491.299   4.030       uce-187+uce-552	0h:0m:0s (0h:0m:0s left)
  20 GTR+F+I+G4   68535.847   4.172       uce-1041+uce-187	0h:0m:0s (0h:0m:0s left)
  21 GTR+F+I+G4   68508.274   12.003      uce-1608+uce-6	0h:0m:0s (0h:0m:0s left)
  22 GTR+F+I+G4   68525.611   18.738      uce-708+uce-72	0h:0m:0s (0h:0m:0s left)
Merging uce-187+uce-552 with BIC score: 68491.299 (LnL: -33269.191  df: 257)
  23 GTR+F+I+G4   68475.667   4.603       uce-1658+uce-187+uce-552	0h:0m:0s (0h:0m:0s left)
  24 GTR+F+I+G4   68481.269   4.336       uce-1288+uce-187+uce-552	0h:0m:0s (0h:0m:0s left)
  25 GTR+F+I+G4   68472.502   4.694       uce-1288+uce-1658	0h:0m:0s (0h:0m:0s left)
Merging uce-6+uce-907 with BIC score: 68436.456 (LnL: -33283.563  df: 246)
  26 GTR+F+I+G4   68396.321   4.176       uce-1041+uce-1288	0h:0m:0s (0h:0m:0s left)
  27 GTR+F+I+G4   68398.703   10.117      uce-1608+uce-252	0h:0m:0s (0h:0m:0s left)
  28 GTR+F+I+G4   68389.849   10.614      uce-1608+uce-6+uce-907	0h:0m:0s (0h:0m:0s left)
Merging uce-1608+uce-6+uce-907 with BIC score: 68389.849 (LnL: -33302.053  df: 235)
  29 GTR+F+I+G4   68354.837   10.313      uce-1608+uce-252+uce-6+uce-907	0h:0m:0s (0h:0m:0s left)
Merging uce-1041+uce-1288 with BIC score: 68349.714 (LnL: -33323.780  df: 224)
  30 GTR+F+I+G4   68359.188   4.353       uce-1041+uce-1288+uce-187+uce-552	0h:0m:1s (0h:0m:0s left)
  31 GTR+F+I+G4   68318.851   4.548       uce-1041+uce-1288+uce-1658	0h:0m:1s (0h:0m:0s left)
Merging uce-708+uce-72 with BIC score: 68316.336 (LnL: -33348.885  df: 213)
Merging uce-1041+uce-1288+uce-1658 with BIC score: 68285.473 (LnL: -33375.248  df: 202)
  32 GTR+F+I+G4   68295.763   4.560       uce-1041+uce-1288+uce-1658+uce-187+uce-552	0h:0m:1s (0h:0m:0s left)
Merging uce-1608+uce-252+uce-6+uce-907 with BIC score: 68250.461 (LnL: -33399.536  df: 191)
Agglomerative model selection: (((uce-1041,uce-1288)4:68349.7,uce-1658)6:68285.5,((uce-1608,(uce-6,uce-907)2:68436.5)3:68389.8,uce-252)7:68250.5,(uce-187,uce-552)1:68491.3,(uce-708,uce-72)5:68316.3,uce-861)
Merging into 5 partitions...
  33 K2P+G4       1931.946    uce-861	0h:0m:2s (0h:0m:-1s left)
  34 TIM3e+G4     6998.077    uce-187+uce-552	0h:0m:3s (0h:0m:-1s left)
  35 SYM+I+G4     19266.453   uce-708+uce-72	0h:0m:10s (0h:0m:-2s left)
  36 TIMe+R4      26545.349   uce-1608+uce-252+uce-6+uce-907	0h:0m:11s (0h:0m:-3s left)
  37 TVMe+G4      12178.828   uce-1041+uce-1288+uce-1658	0h:0m:13s (0h:0m:-3s left)
Best partition model BIC score: 68004.086 (LnL: -33363.736  df:168)
Partition information was printed to astral_pta_75p.best_scheme.nex
Partition information in Raxml format was printed to astral_pta_75p.best_scheme

All model information printed to astral_pta_75p.model.gz
CPU time for ModelFinder: 152.218 seconds (0h:2m:32s)
Wall-clock time for ModelFinder: 52.728 seconds (0h:0m:52s)
Generating 1500 samples for ultrafast bootstrap (seed: 194023)...

NOTE: 19 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -33368.186
Current log-likelihood at step 1: -33362.052
Current log-likelihood at step 2: -33361.360
Current log-likelihood at step 3: -33361.195
Current log-likelihood at step 4: -33361.112
Partition-specific rates:  0.484 0.777 0.426 2.173 0.232
Parameters optimization took 3 rounds (0.412 sec)

Computing ML distances based on estimated model parameters...
Computing ML distances took 0.000431 sec (of wall-clock time) 0.001673 sec(of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Computing RapidNJ tree took 0.056876 sec (of wall-clock time) 0.167414 sec (of CPU time)
Log-likelihood of RapidNJ tree: -43893.801
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.660 second
Computing log-likelihood of 98 initial trees ... 1.519 seconds
Current best score: -33361.112

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -33357.671
Current log-likelihood at step 1: -33357.495
Current log-likelihood at step 2: -33357.455
Parameters optimization took 1 rounds (0.207 sec)

BETTER TREE FOUND at iteration 1: -33357.455
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -33357.429
Current log-likelihood at step 1: -33357.350
Parameters optimization took 0 rounds (0.105 sec)

BETTER TREE FOUND at iteration 2: -33357.350
Iteration 10 / LogL: -33366.994 / Time: 0h:0m:7s
Iteration 20 / LogL: -33358.743 / Time: 0h:0m:11s
Finish initializing candidate tree set (12)
Current best tree score: -33357.350 / CPU time: 10.714
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -33357.328
Current log-likelihood at step 1: -33357.316
Parameters optimization took 0 rounds (0.096 sec)

UPDATE BEST LOG-LIKELIHOOD: -33357.316
Iteration 30 / LogL: -33357.909 / Time: 0h:0m:15s (0h:0m:39s left)
Iteration 40 / LogL: -33358.457 / Time: 0h:0m:19s (0h:0m:31s left)
Iteration 50 / LogL: -33391.050 / Time: 0h:0m:23s (0h:0m:25s left)
Log-likelihood cutoff on original alignment: -33437.426
Iteration 60 / LogL: -33365.000 / Time: 0h:0m:27s (0h:0m:19s left)
Iteration 70 / LogL: -33357.387 / Time: 0h:0m:31s (0h:0m:14s left)
Iteration 80 / LogL: -33357.411 / Time: 0h:0m:35s (0h:0m:9s left)
Iteration 90 / LogL: -33386.353 / Time: 0h:0m:39s (0h:0m:5s left)
Iteration 100 / LogL: -33357.997 / Time: 0h:0m:43s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -33437.426
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.999
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:45s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Initial log-likelihood: -33357.316
Current log-likelihood at step 1: -33357.312
Partition-specific rates:  0.478 0.772 0.420 2.189 0.230
Parameters optimization took 0 rounds (0.097 sec)

Partition information was printed to astral_pta_75p.best_model.nex
BEST SCORE FOUND : -33357.312

Testing tree branches by SH-like aLRT with 1500 replicates...
0.867 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file astral_pta_75p.splits.nex
Total tree length: 10.202

Total number of iterations: 103
CPU time used for tree search: 208.731 sec (0h:3m:28s)
Wall-clock time used for tree search: 45.063 sec (0h:0m:45s)
Total CPU time used: 215.671 sec (0h:3m:35s)
Total wall-clock time used: 47.012 sec (0h:0m:47s)

Computing bootstrap consensus tree...
Reading input file astral_pta_75p.splits.nex...
70 taxa and 359 splits.
Consensus tree written to astral_pta_75p.contree
Reading input trees file astral_pta_75p.contree
Log-likelihood of consensus tree: -33357.312

Analysis results written to: 
  IQ-TREE report:                astral_pta_75p.iqtree
  Maximum-likelihood tree:       astral_pta_75p.treefile
  Likelihood distances:          astral_pta_75p.mldist
  Best partitioning scheme:      astral_pta_75p.best_scheme.nex
           in RAxML format:      astral_pta_75p.best_scheme

Ultrafast bootstrap approximation results written to:
  Split support values:          astral_pta_75p.splits.nex
  Consensus tree:                astral_pta_75p.contree
  Screen log file:               astral_pta_75p.log

Date and Time: Thu Sep 18 06:55:09 2025
